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Lecture 15 Flashcards

1
Q

How are Quaternary Structures named?

A

By the number and type of subunits ex. 2 subunits is a dimer

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2
Q

What is a Homodimer?

A

A quaternary structure with two identical subunits

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3
Q

What is a Heterodimer?

A

A quaternary structure with two non-identical subunits

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4
Q

What stabilizes 4º strucutre?

A

The same forces as Tertiary structure
•Hydrophobic interactions
•H-bonds, ion pairs fine tune them

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5
Q

Where are Hydrophobic interactions predominant in quaternary structure?

A

Where the different subunits are in contact with each other in the overall tertiary structure

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6
Q

What kind of bonds are not necessary in Quaternary Strucutre?

A

Covalent bonds

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7
Q

What are the two subunits that hemoglobin contains?

A

Two alpha and two beta

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8
Q

What kind of Quaternary Structure can hemoglobin be described as?

A

A heterotetramer

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9
Q

What is the function of a protein determined by?

A

Its strucutre

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10
Q

What is the three-dimensional structure of a protein determined by?

A

Its 1º structure (the sequence of the amino acids in the polypeptide chain)

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11
Q

What kind of 4º is Myoglobin?

A

A monomer

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12
Q

What kind of 4º is Hemoglobin?

A

An Oligomer

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13
Q

What kind of Amino acids would we expect to be on the inside if a polypeptide structure?

A

Non-polar hydrophobic amino acids

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14
Q

What are both Hemoglobin and Myoglobin involved in?

A

Reversible oxygen binding

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15
Q

What does Hemoglobin in RBCs do?

A

Binds to O2 in the lungs and releases it in the tissues

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16
Q

Where does Myoglobin bind to O2?

A

Im muscles cells

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17
Q

What is the difference between oxygen binding of Hemoglobin and Myoglobin?

A

They bind to O2 with different affinities and under different conditions

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18
Q

What kind of cells is Myoglobin found in?

A

Myocytes

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19
Q

What is Myoglobin involved in in myocytes?

A

Transporting oxygen from the cell membrane to the mitochondria

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20
Q

What takes oxygen from the lungs to the peripheral tissue?

A

Hemoglobin

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21
Q

What acts as a local reserve of O2 during intense exercise?

A

Myoglobin

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22
Q

What stores O2 in aquatic animals?

A

Myoglobin

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23
Q

What kind of interaction is it when Myoglobin binds to oxygen?

A

Simple ligand binding

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24
Q

What is the equilibrium in free ligang binding?

A

There is an equilibrium of the ligand binding to the protein and the ligand-protein complex

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25
What occurs in the dissociation process of the protein-ligand complex?
The protein-ligand complex dissociates into free protein and free ligand
26
What is Kd?
The dissociation constant
27
What is the equation of the dissociation constant?
The concentration of the the free ligand and the concentration of the free protein multiplied. This is all divided by the concentration of the ligand protein complex
28
What does it mean if the ligand has a strong affinity for the protein?
Dissociation is less favored because the complex is stable
29
How is Kd affected by affinity?
Kd gets smaller as affinity increases
30
How does Kd affect the stability of a protein ligand complex?
The smaller the Kd the more stable the protein ligand complex is
31
What is on the X and Y axis of ligand binding curves?
The X axis is the concentration of the Ligand and the Y axis is the percent saturation of the Protein
32
Why is there a Plateau on Ligand Binding curves?
Because there isn't anymore protein to bind to that ligand and so the proteins are reaching 100% saturated
33
What kind of approach is the plateau of a ligand binding curve?
An asymptotic approach
34
Why does a Hyperbolic binding curve occur?
Because there is an unchanging affinity between the ligand and protein
35
What is the Affinity like in Asymptotic Binding curves?
Affinity is constant
36
Where is the Ligand Protein affinity not constant?
In Allosteric binding curves
37
What is equal to the value of Kd?
50% bound to a particular ligand
38
How is the %saturation affected by Kd?
The smaller the value of Kd the more you would expect to be bound to the protein at a particular concentration
39
What would have a higher affinity in terms of ligand binding to a protein and Kd?
A lower Kd would have a higher affinity
40
With what kind of affinity does myoglobin bind to oxygen?
With constant affinity
41
What does Myoglobin bind to?
Oxygen
42
What is the Tertiary structure of Myoglobin?
A single polypeptide chain (with alpha helices and irregular structure) that is associated with a heme prosthetic group
43
How many helices are in the structure of myoglobin?
Eight helices (A through H)
44
What is the prosthetic group in Myoglobin?
The heme group
45
What is responsible for binding of the oxygen in Myoglobin?
The heme group
46
What kind of molecule is heme?
It is an organic molecule that contains an organic molecule
47
What is the shape of Heme?
It is circular and planar
48
What is the polarity of heme?
For the most part it is quite hydrophobic with two polar/charged carboxyl groups so it is amphipathic
49
What happens to the hydrophobic portion of heme?
It is tucked into a hydrophobic binding pocket
50
What is exposed to solvent in Heme?
The two Propionyl groups (the groups containing carboxylic acids)
51
Which myoglobin helices is the hydrophobic pocket found between?
Helices E and F
52
Why is Heme a delocalized structure?
Because of its conjugated double bonds
53
What level structure are prosthetic groups a part of?
Tertiary structure
54
Where do the four nitrogens around the iron in heme come from?
The overall heme structure
55
How many structures does the iron in heme have a preferred interaction with?
Six different coordinating structures
56
Where do four of the places that the iron in heme bind with come from?
The Heme
57
What is the 5th coordination position on heme occupied by?
A nitrogen in the side chain of histidine
58
What is the Proximal histidine?
The histidine in the 5th coordination position of heme
59
What is the 6th coordination position of heme occupied by?
Oxygen
60
What is the Porphyrin ring held in place by?
Hydrophobic interaction by coordination bond between iron and a histidine
61
What are the other names for the Proximal Histidine?
His 93 | His F8
62
What are the functions of the proximal histidine?
* It is an additional binding interaction of heme into the binding pocket to make sure heme stays tightly associated with the polypeptide and doesn't end up dissociating from the structure * Ensures the iron remains in the correct oxidation state for the binding of oxygen
63
What is found in the 6th coordination position?
Oxygen
64
What does is meant by histidine and oxygen coordinate the heme group?
The bind to the overall structure to prevent it from dissociating
65
How does oxygen bound to heme coordinate the iron atom?
It uses one of its lone pairs and H bonds to an H bound to N on the distal histidine
66
What are the other names for the Distal Histidine?
* Histidine 64 | * Histidine E7
67
What does the distal histidine do?
Forms a H-bonding interaction with the oxygen atom at the 6th coordination position
68
What happens every time we create a favorable interaction between the protein and ligand what is the result?
An increase in the affinity
69
What is the function of the distal histidine binding?
* Increases oxygen binding affinity * Lowers affinity for other molecules * Increases specificity for oxygen
70
What is the affinity of carbon monoxide for the heme in relation to oxygen?
Carbon monoxide has a way higher affinity for heme than oxygen
71
What is specificity?
Preference for binding one thing relative to another thing
72
What other amino acids create specificity for the oxygen molecule besides the distal histidine?
Phe and Val
73
What are the binding sites in myoglobin designed to do?
Optimize binding specificity and affinity
74
What is the difference in binding between oxygen and carbon monoxide binding to the 6th coordination position?
O2 binds at an angle and carbon monoxide binds in a straight line and occupies the same place of E7 increasing specificity for oxygen

Biocheem (38 decks)

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